A . N . A: 2014

::PROTEIN DATA BANK::

Assalamualaikum!

Alhamdulillahirrabil alamin.

Gratitude we bid to Allah because giving us

another opportunity to live on this earth to worship Him

This post is specifically for my KOS 1110 assignment

Have you ever heard about Protein Data Bank??

Well then in this entry , I am going to give you just a brief explanation..:)

Introduction

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologistsand biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently.

HISTORY

The PDB was established in 1971 at Brookhaven National Laboratory under the leadership of Walter Hamilton and originally contained 7 structures. After Hamilton's untimely death, Tom Koetzle began to lead the PDB in 1973, and then Joel Sussman in 1994. In 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) became responsible for the management of the PDB. In 2003, the wwPDB was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. It consists of organizations that act as deposition, data processing and distribution centers for PDB data.

X Ray Crystallography

X-ray crystallography is a method of determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of X-rays to diffract into many specific directions. By measuring

the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal.

Protein Structures

Following are the image of protein retrieved from protein data bank:-

HTML Tables

	Description
Molecule	Thermosylin
Type	protein
Length	316
Weight	35646.59
Polymer	1

Sources:-
1. http://www.rcsb.org/pdb/home/home.do
2. http://en.wikipedia.org/wiki/Protein_Data_Bank

XML : Extensible Market Language

Assalamualaikum!

Alhamdulillahirrabil alamin.

Gratitude we bid to Allah because giving us

another opportunity to live on this earth to worship Him

This week we learned about Extensible Market Language (XML). Basically, XML is use to transport and store data and focus on what data is. Sometimes people confused XML with HTML. XML is not a replacement for HTML but both of them use a similar language. XML also can be described as a software and hardware independent tool for carrying information.

Differences between HTML and XML

HTML	XML
designed to display data	designed to transport and store data
focus on how data looks	focus on what data is
displaying information	carrying information

Example :

Input

<note>

<to>Amirul</to>

<heading>Greeting</heading>

<body>Welcome to the new mahallah!</body>

</note>

Output

To: Amirul

From: Anas

Greeting: Welcome to the new mahallah!

Function XML

Simplifies data sharing
Simplifies platform changes
Makes your data more available
Create new Internet languages

XML Tree

XML documents form a tree structure that starts at "the root" and branches to "the leaves".

To see tutorial for XML for beginner [click here]

For more info about XML you can visit this page : http://www.xmlfiles.com/xml/

Internet History...

Assalamualaikum

Alhamdulillahirrabil alamin.

Gratitude we bid to Allah because giving us

another opportunity to live on this earth to worship Him

Today we will learn about history of internet, here are some story that we may understand.

In the late 1950's the Advanced Research Projects Agency (ARPA) was founded in the United States with the primary focus of developing information technologies that could survive a nuclear attack. In 1967 ARPA university and private sector contractors met with representatives of the Department of Defense to discuss possible protocols for sharing information via computers. In 1969, two years before the calculator was introduced to consumers ( History of the Internet and WWW ) and the year after National Public Radio was established, the precursor of the Internet, ARPANET, was born. It connected four sites at the University of California at Los Angeles, the University of California at Santa Barbara, Stanford Research Institute, and the University of Utah. Throughout the 1970's researchers concentrated on developing protocols for controlling networks, moving messages across a system of networks, and allowing for remote access to the networks. There were computers connected at about two dozen sites when the first email was sent in 1972, but the number of sites and messages soon mushroomed. By 1975 there were 63 sites. In 1980, 200 host computers were connecting 20,000 people at university, military, and government locations. Twelve years later the number of hosts had grown to more than a million internationally, and in January of 1999 there were more than 43 million. ( Hobbes' Internet Timeline v4.1 )

If the 1970's were a time of research, the 1980's were a time of development. The TCP/IP protocol was introduced in 1983, and at the University of Wisconsin the name server was developed. The next year domain name server (DNS) was established. In 1986, the National Science Foundation developed a system to connect the growing number of hosts. Regional networks were connected to a backbone network, which became known as the NSFNET. As the "Internet" continued to grow and prosper, ARPANET came to an end in 1989 just before HTML protocol was introduced in 1990. HTML allowed graphics to be sent along with text to create hypertext pages customized to the sender's preference. Everything was now in place for explosive growth.

HOW INTERNET WORK

Internet protocol

Every machine on the Internet has a unique identifying number, called an IP Address. The IP stands for Internet Protocol, which is the language that computers use to communicate over the Internet. A protocol is the pre-defined way that someone who wants to use a service talks with that service. The "someone" could be a person, but more often it is a computer program like a Web browser.

To make it easier for us humans to remember, IP addresses are normally expressed in decimal format as a dotted decimal numberlike the one above. But computers communicate in binary form. Look at the same IP address in binary:

The four numbers in an IP address are called octets, because they each have eight positions when viewed in binary form. If you add all the positions together, you get 32, which is why IP addresses are considered 32-bit numbers. Since each of the eight positions can have two different states (1 or zero), the total number of possible combinations per octet is 28 or 256. So each octet can contain any value between zero and 255. Combine the four octets and you get 232 or a possible 4,294,967,296 unique values!

Out of the almost 4.3 billion possible combinations, certain values are restricted from use as typical IP addresses. For example, the IP address 0.0.0.0 is reserved for the default network and the address 255.255.255.255 is used for broadcasts.

The octets serve a purpose other than simply separating the numbers. They are used to create classes of IP addresses that can be assigned to a particular business, government or other entity based on size and need. The octets are split into two sections: Net and Host. The Net section always contains the first octet. It is used to identify the network that a computer belongs to. Host (sometimes referred to as Node) identifies the actual computer on the network. The Host section always contains the last octet. There are five IP classes plus certain special addresses.

Here are some example how to using a binary digit.

Number in base 2	2⁸	2⁷	2⁶	2⁵	2⁴	2³	2²	2¹	2⁰
Number in base 10	256	128	64	32	16	8	4	2	1

If my IP address is 210.48.221.4

that mean,

210=128+64+16+2 : 11010010

48=32+16 : 00011000

221=128+64+16+8+4+1 : 11011101

4=4 : 000000100

that mean my 32-bit is 110100100001100011011101000000100

for more info, visit
link 1
link 2

HTML-er wannabe

~HTML~

Assalamualaikum!

Alhamdulillahirrabil alamin.

Gratitude we bid to Allah because giving us

another opportunity to live on this earth to worship Him

HTML stands “Hypertext Markup Language”

HTML is the language behind the web, the thing that your web browser interprets in order to display text and images. Writing an HTML document doesn't require expensive software, it can be done for free in a regular text editor (e.g. Windows: Notepad, Notepad++; Mac: TextEdit, TextWrangler).

An HTML document in its simplest form can be written:

<html>My first HTML document</html>

The angle brackets are important, they contain the "tag" that describes the content. Tags are "paired", i.e. there is an opening tag and a closing one. The closing one is identical except for the forward slash.

This standardized language of computer code,embedded in “source”documents behind all web documents and formatting instructions for display on the screen.It embeds within it other programming languages and applications such as SGML, XML, Java Script and more.This language gives authors the means to following features.

Publish online documents with headings,text,tables,lists,photos etc.
Retrieve online information via hypertext links,at the click of button.
Design forms for conducting transaction with remote services,for use in searching for information, making reservations, ordering products etc.
Include spread sheets,video clips,sound clips and other applications directly in their documents.

HISTORY OF HTML

HTML was developed by Tim Berners-Lee while at the “European Organization for Nuclear Research” , known as CERN is a European research organization whose purpose is to operate the world’s largest particle physics laboratory.Html was popularized by the Mosaic browser.At that time the Web depends on web page authors and vendors the same conventions for HTML.This has motivated joint work on specifications for hyper text markup language.
HTML 2.0 was developed under the aegis of the internet engineering task force on November 1995. HTML + and HTML 3.0 proposed much richer versions of HTML. Hyper Text Markup Language document should work well across different web browsers.

Some HTML tagname and it use.

h1 to h6	Headings
p	Paragraphs
a	Links
img	Images

Here are some video that maybe useful for our study.

ChemSketch

Assalamualaikum!

Alhamdulillahirrabil alamin.

Gratitude we bid to Allah because giving us

another opportunity to present this entry on the topic CHEMSKETCH

Just to recap on the 30th October 2014 , our class had learned something that are new for most of us (I guess!!) . As you can see from the entry topic I will focusing more on ChemSketch

I will just give a brief explanation regarding ChemSketch . Basically ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.

This software is very useful for lecturers/ teaches in using it for aids of teaching

At first when you open the software it will appears the same as in the picture below . To start drawing you need to switch to draw mode(Top left hand side of software).

Alhamdulillah within the 3 hours given to us we are able to complete to draw some graphical objects using ChemSketch as listed below:

Energy of reaction diagram
Orbitals
Vacuum Distillation Apparatus
Two-chain DNA Strand
Lipids

Here are some drawings that we had done with the help of my team members according to the list above:

1)Energy of reaction diagram

The challenge that we had encountered in this part is drawing the word"Chemistry" manually and must be as nice as possible

Instructions:

Switch to Draw mode and click Polyline .

then

use same polyline to draw x & y axis

2)Orbitals

Types Of Orbitals

Instructions:

Make sure you are in the draw mode and click Polygon .

3)Vacuum Distillation Apparatus

Instructions:

In the Template Window , from the Template list, choose Lab Kit.

then,

add text and callouts to explain the apparatus

4)Two-chain DNA Strand

Instructions:

This drawing also using the polyline.

5)Lipids

Instructions:

Click Ellipse for the circle

and

polyline for carbonic tail

Benefits of using this tool:

Visualize chemical structures in 2D or 3D to gain more insight into spatial configurations, and relationships to molecular properties
Create professional reports, working with structures, text, and graphics simultaneously

ACD/ChemSketch also allows you to check other tautomeric forms for your drawn structure. Consideration of tautomeric forms is very important for structure searching, predictions (such as physicochemical properties, i.e., pK_a), and interpretation (i.e., of NMR, MS, and other analytical data).

There are several links to download this ACD Chemsketch

Here are some links for the tutorial on how to use ChemSketch:

Publisher	Advanced Chemistry Development
Publisher web site	http://www.acdlabs.com/
Release date	November 07, 2013
Operating systems	Windows 7, Windows 8, Windows XP
Category	Educational Software